But Boeing said the plane was still on track to fly this year. The company blamed its loss also on an additional charge related to its delayed 747 program.
To reflect the 787 and 747 impacts, earnings guidance for 2009 has been changed to a range of $1.35 to $1.55 per share, from $4.70 to $5.00 previously.
Boeing shares were down about 2 percent in premarket trade.
The 787 cost reclassification and the 747 charge for increased costs and difficult market conditions clearly overshadowed what continues to be otherwise solid performance across our commercial production programs and defense business, said Boeing Chief Executive Jim McNerney in a statement.
We look forward to getting the 787 and 747-8 in the air soon and moving forward with flight test and certification for these two important programs, he said in a statement.
The world's second-largest plane-maker, after EADS
Excluding a loss from discontinuing operations, Boeing reported a loss of $2.22 per share, compared with analysts' estimates for a loss of $2.12 per share, according to Thomson Reuters I/B/E/S.
The latest results reflect the reclassification, to research and development, of costs incurred through July for the first three 787 flight-test airplanes, spending on those planes for August and September, and the 747 charge.
Revenue rose 9 percent to $16.7 billion. The year-ago period was impacted by a labor strike.
Revenue from its commercial airplane division increased 13 percent to $7.9 billion on higher deliveries. The division booked 96 gross orders during the quarter, while 17 orders were canceled. Contractual backlog was $254 billion.
Boeing's Integrated Defense Systems saw third-quarter revenue up 3 percent to $8.7 billion on increased military aircraft deliveries.
The company said the first flight of the long delayed 787 Dreamliner remains on track to occur by the end of 2009, with first delivery scheduled for the fourth quarter of 2010.
Shares of Boeing, a Dow component were down 2 percent to $50.84 in premarket trade.
(Reporting by Kyle Peterson; editing by John Wallace, Dave Zimmerman)